Convert to Glycan Composition — as_glycan

Converts an object to a glycan composition using vctrs casting framework. This function provides a convenient way to convert various input types to glycan_composition().

Usage

as_glycan_composition(x)

Arguments

x

An object to convert to a glycan composition. Supported inputs include:

Named integer vectors or lists of named integer vectors
Character vectors with composition strings (e.g., "Hex(5)HexNAc(2)")
glyrepr_structure objects (counts both monosaccharides and substituents)
Existing glyrepr_composition objects (returned as-is)

Value

A glyrepr_composition object.

Details

This function uses the vctrs casting framework for type conversion. When converting from glycan structures, both monosaccharides and substituents are counted. Substituents are extracted from the sub attribute of each vertex in the structure. For example, a vertex with sub = "3Me" contributes one "Me" substituent to the composition.

Examples

# From a single named vector
as_glycan_composition(c(Hex = 5, HexNAc = 2))
#> <glycan_composition[1]>
#> [1] Hex(5)HexNAc(2)

# From a list of named vectors
as_glycan_composition(list(c(Hex = 5, HexNAc = 2), c(Hex = 3, HexNAc = 1)))
#> <glycan_composition[2]>
#> [1] Hex(5)HexNAc(2)
#> [2] Hex(3)HexNAc(1)

# From a character vector of Byonic composition strings
as_glycan_composition(c("Hex(5)HexNAc(2)", "Hex(3)HexNAc(1)"))
#> <glycan_composition[2]>
#> [1] Hex(5)HexNAc(2)
#> [2] Hex(3)HexNAc(1)

# From a character vector of simple composition strings
as_glycan_composition(c("H5N2", "H5N4S1F1"))
#> <glycan_composition[2]>
#> [1] Hex(5)HexNAc(2)
#> [2] Hex(5)HexNAc(4)dHex(1)NeuAc(1)

# From an existing composition (returns as-is)
comp <- glycan_composition(c(Hex = 5, HexNAc = 2))
as_glycan_composition(comp)
#> <glycan_composition[1]>
#> [1] Hex(5)HexNAc(2)

# From a glycan structure vector
strucs <- c(n_glycan_core(), o_glycan_core_1())
as_glycan_composition(strucs)
#> <glycan_composition[2]>
#> [1] Man(3)GlcNAc(2)
#> [2] Gal(1)GalNAc(1)